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Table 3 Summary of advantages and disadvantages of strategies for direct RNA sequencing of RNA viruses

From: A novel method for the capture-based purification of whole viral native RNA genomes

Strategy type Employed in Advantages Disadvantages
1. Custom adapter – Keller et al. (2018) – Highest sequencing specificity
– Rapid turnaround time
– Cannot sequence fragmented RNA
– Foreknowledge of target sequence required
2. Conventional adapter – Wongsurawat et al. (2019)
– Pre-capture group
– Sequences fragmented RNA
– No foreknowledge of target sequence
– Rapid turnaround time
– Low sequencing specificity
3. Conventional adapter + capture – Post-capture group
Concentrated post capture group
– Sequences fragmented RNA
– Less foreknowledge of target sequence required
– Higher sequencing specificity
– Increased turnaround time
4. Conventional adapter + host rRNA depletion – Wongsurawat et al. (2019) – Sequences fragmented RNA
– No foreknowledge of target sequence
– Fast turnaround time
– Low sequencing specificity